Profiling of microRNA transcripts in mouse plasma samples

MARKET RESEARCH PURPOSES ONLY NOT A REQUEST FOR PROPOSAL OR SOLICITATION The U.S. Food and Drug Administration (FDA), is conducting market research to support the National Center for Toxicological Research (NCTR) requirement for profiling of microRNA transcripts in mouse plasma samples after treatment with sunitinib. The FDA is seeking small business sources to determine the availability and capability of small businesses capable of providing the required services. Other than small business concerns are also encouraged to submit capability statements. The following information is provided to assist the FDA in conducting Market Research to identify potential contractors for this effort: The associated North American Industry Classification System (NAICS) Code is-541690- Other Scientific and Technical Consulting Services; Small Business Size Standard is $16.5 million. Statement of Work (SOW): Profiling of microRNA transcripts in mouse plasma samples after treatment with sunitinib. Background NCTR is in need of identification of early predictive biomarkers of sunitinib-induced cardiac damage. Sunitinib is a tyrosine kinase inhibitor approved for treatment of cancers such as renal cell carcinoma, imatinib-resistant gastrointestinal stromal tumor, and pancreatic neuroendocrine tumors. Recent clinical studies have shown that patients treated with sunitinib are at increased risk of developing cardiac dysfunction. The most common adverse effects of sunitinib are decrease of left ventricular ejection fraction (LVEF), hypertension and delayed ventricular repolarization interval prolongation in patients. However, the multi-target nature of sunitinib at therapeutically relevant concentrations makes it difficult to identify the precise mechanism of cardiotoxicity. Many aspects of sunitinib-induced cardiotoxicity such as on/off target toxicities and the interactions of related pathways are still not fully understood. There is also a lack of information related to sex-based differential cardiotoxicity induced by sunitinib. Currently, there are no clinical biomarkers to predict sunitinib-induced cardiotoxicity during cancer therapy. Thus, there is a need for identification of novel biomarkers capable of predicting early cardiotoxicity induced by sunitinib. Use of early cardiotoxicity biomarkers will prove valuable in identification of cancer population at risk for future heart failure so that effective cardioprotective interventions can be implemented sooner to minimize or prevent sunitinib-induced cardiotoxicity. This will enhance FDA’s goal to protect and promote individual health. Additionally, these early biomarkers will allow accurate prediction and minimize the risks associated with FDA-regulated products. Additionally, profiling of microRNAs using highly sensitive high throughput sequencing technology in plasma samples from mice treated with sunitinib will aid in discovery of novel circulating miRNAs released in plasma prior to the onset of myocardial injury or pathology. These miRNAs can serve as early predictive biomarkers of cardiotoxicity and may have potential in identifying cancer patients or survivors at risk of future heart damage in clinics. Results from the miRNA profiling will facilitate identification of novel early preclinical markers of sunitinib-induced cardiotoxicity. Purpose The purpose of this procurement is for services to measure large number (~2,000) of microRNA (miRNA; these molecules regulate expression of thousands of genes) transcripts using a sensitive high throughput genomics (HTG) technology in mouse plasma samples treated with sunitinib to aid in discovery of novel miRNAs released in plasma prior to the onset of cardiac injury. These miRNAs can be used as early predictive biomarkers of cardiotoxicity and may prove valuable in identifying cancer patients or survivors susceptible at risk for future heart damage and/or designing new interventions to minimize cardiotoxicity tailored to susceptible sub-population. Therefore, a highly specific and sensitive miRNA Whole Transcriptome Assay (WTA) is required to accomplish our goal. Period of Performance Work and deliverable shall be within 60 calendar days of receipt of government furnished samples. The Government will send the 120 plasma samples within 30 calendar days of award. Location of Performance Contractor’s Facility Scope and Requirements The contractual service must use miRNA WTA technology that shall meet the followings: Contractor shall utilize robust, automated HTG system coupled with the sensitivity and dynamic range of next-generation sequencing (NGS)-based detection. Contractor shall utilize HTG technology that is a combination of nuclease protection assay and NGS for targeted sequencing to provide accurate and sensitive measurement of the expression. Contractor shall utilize HTG system to eliminate biases associated with DNA/RNA extraction, size selection, cDNA synthesis, and adapter ligation for reproducible results. Contractor shall be capable of extraction-free sample preparation (without the need for RNA extraction) in or mouse plasma. Contractor shall be capable of simultaneous, quantitative detection of ~2000 miRNA transcripts in a small volume of human or mouse plasma (15 µl). Contractor shall be capable of running up to 100 - 200 plasma or RNA samples simultaneously in a 96-well plate and must provide fast, reliable, reproducible, and quantitative analysis of ~2000 targeted miRNAs in a single assay. All samples must be profiled under the same conditions at the same time to obtain reliable results. Contractor shall use sophisticated HTG informatics package to significantly simplify data analysis and simplified data output in Excel format. When sequencing the samples, the read length shall be a minimum of 75 bp with at least 1 million of reads per sample. All data (raw and normalized) must to be provided to NCTR in a Microsoft Excel format within 60 calendar days after receiving the 120 plasma samples. The remainder of samples shall be shipped back to NCTR in dry ice using commercial carrier paid by the Contractor. Deliver to: Attn: to be complete at time of award. FDA NCTR 3900 NCTR Road Jefferson, AR 72079 FOB Point destination. All items shall include delivery to the destination identified herein. The offeror shall furnish sufficient technical information necessary for the Government to conclusively determine that the offered products/services and components meet the technical requirements identified above. Though the target audience is small business manufacturers or small businesses capable of supplying a U.S. made product of a small business manufacturer or producer all interested parties may respond. At a minimum, responses shall include the following: Business name, DUNS number, business address, business website, business size status (i.e., SB, VOSB, SDVOSB, HUBZone SB, SDB, WOSB, LB), point of contact name, mailing address (if different from business address), phone number and email address (Provide this same information if responding to provide a product manufactured by another firm); Sufficient descriptive literature that unequivocally demonstrates that offered services can meet the above requirements. All descriptive material necessary for the government to determine whether the service/product offered meets the technical requirements including: technical specifications, descriptive material, literature, brochures and other information, which demonstrates the capabilities of the contractor to meet the requirement. Provide what High throughput genomics (HTG) platform is to be used and what highly specific and sensitive miRNA Whole Transcriptome Assay (WTA) will be used. Provide recent (within the last three (3) years) and relevant prior experience information for which the offeror has provided same or substantially similar miRNA profiling service solutions and used for same or near-same applications including HTG platform and miRNA WTA as set forth herein. Offeror should detail similar scope, complexity and magnitude. For each reference include period of performance, description (how is this relevant to current requirement), dollar value, your role and responsibilities as either a prime or subcontractor , client name, client address, client point of contact name, client point of contact phone number, and client point of contact email address. Respondents who do not provide a valid email address for the POC may be evaluated negatively. If applicable, identification of the firm's GSA Schedule contract(s) by Schedule number and SINs that are applicable to this potential requirement. Provide information if any of these specifications are too restrictive. No response will be considered that the listed specifications are adequate in a competitive environment. If a large business, identify the subcontracting opportunities that would exist for small business concerns; Standard commercial warranty and payment terms; and Though this is not a request for quote, informational pricing is required. The government is not responsible for locating or securing any information, not identified in the response. The Government encourages any comments and/or suggestions from any interested party, regarding the specifications. While the Government will not respond directly to your comments and/or suggestions; we will consider them as we finalize the specifications in preparation for the forthcoming solicitation. Interested Parties shall respond with capability statements which are due in person, by postal mail or email to the point of contact listed below on or before March 24, 2020 by 13:00 hours (Central Time in Jefferson, Arkansas) to [email protected] , or mail to the Food and Drug Administration, OO/OFBA/OAGS/DAP, Attn: Nick Sartain, 3900 NCTR Road, Building 50, Room 422, Jefferson, AR 72079-9502. Reference FDA1225287. Notice of Intent Responses to this sources sought announcement will assist the Government in determining whether or not any future requirement similar to this one should be set aside for small business, made available to full and open competition or procure through sole-source acquisition procedures. Disclaimer and Important Notes This notice does not obligate the Government to award a contract or otherwise pay for the information provided in response. The Government reserves the right to use information provided by respondents for any purpose deemed necessary and legally appropriate. Any organization responding to this notice should ensure that its response is complete and sufficiently detailed to allow the Government to determine the organization’s qualifications to perform the work. Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. After a review of the responses received, a pre-solicitation synopsis and solicitation may be published in FedBizOpps. However, responses to this notice will not be considered adequate responses to a solicitation. Confidentiality No proprietary, classified, confidential, or sensitive information should be included in your response. The Government reserves the right to use any non-proprietary technical information in any resultant solicitation(s).